Data and R Code for: Proximate, Anti-Nutrient, and Mineral-Bioavailability Profile of Carrot (Daucus carota L.) under Variety, Poultry Manure, and Tillage Management in a Tropical Environment

Overview This repository contains the raw laboratory data and R analysis script supporting the manuscript above. The trial assessed two carrot varieties grown under three poultry manure rates and two tillage systems in a split-split-plot field experiment at Nsukka, southeastern Nigeria, replicated three times. Mineral and vitamin results from the same trial were analysed separately and have already been published in: Anozie CC, et al. (2024). Assessment of Mineral and Vitamin Contents of Carrot (Daucus carota L.) as Influenced by Poultry Manure, Variety and Tillage. Tropical Journal of Natural Product Research, 8(2). The manuscript accompanying this deposit uses only the proximate and anti-nutrient/phytochemical columns from the same raw dataset, plus the previously published zinc, iron, and calcium values (used only as denominators for the derived phytate:mineral molar ratios reported in Section 3.5 of the manuscript). Files in this deposit File Description New_Chemical_data.xlsx Raw laboratory data, one row per composite root sample (36 rows total) carrot_analysis.R Self-contained R script that reproduces all statistics, tables, and figures in the manuscript README.md This file Experimental design Split-split-plot design, three replications (blocks): Main plot factor - Tillage: Ridge (R) or Bed (B) Sub-plot factor - Poultry manure rate: 0 t/ha (M1), 5 t/ha (M2), or 10 t/ha (M3) Sub-sub-plot factor - Variety: Touchon Mega (T) or Kuroda (K) Each row in New_Chemical_data.xlsx is a composite lab sample (two harvested roots per variety-manure-tillage combination), giving 2 tillage x 3 manure x 2 variety x 3 replicates = 36 rows. Column key for New_Chemical_data.xlsx Column Meaning Codes / Units TILLAGE Tillage system R = Ridge, B = Bed MANURE Poultry manure rate M1 = 0 t/ha, M2 = 5 t/ha, M3 = 10 t/ha VARIETY Carrot variety T = Touchon Mega, K = Kuroda REPS Replicate block 1, 2, or 3 Moisture Moisture content % fresh weight Ash Ash content % fresh weight fat Crude fat content % fresh weight PROTIEN Crude protein content % fresh weight Fibre Crude fibre content % fresh weight OXALATE Oxalate content mg/100 g fresh weight Cynide Cyanide content mg/100 g fresh weight Tannin Tannin content mg/100 g fresh weight Phytate Phytate content mg/100 g fresh weight Saponin Saponin content mg/100 g fresh weight Flevonoid Flavonoid content mg/100 g fresh weight Zinc, Fe, CA Zinc, iron, calcium content mg/100 g fresh weight - from the companion mineral/vitamin publication [see above]; used here only to compute phytate:mineral molar ratios Mg, SE, VIT C, VIT A, K, P, CU Additional mineral/vitamin data from the companion publication Not used in the present manuscript Note: carbohydrate (CHO) is not a raw column - it is calculated by difference in the R script as 100 - (Moisture + Ash + fat + PROTIEN + Fibre). How to run the analysis Install R (version 4.x or later). Install the required packages (one-time): install.packages(c("readxl", "dplyr", "tidyr", "ggplot2", "emmeans",                    "multcompView", "multcomp", "FactoMineR",                    "factoextra", "car")) Place New_Chemical_data.xlsx and carrot_analysis.R in the same folder. Open carrot_analysis.R and edit the data_path variable near the top if your file is not named exactly New_Chemical_data.xlsx. Run the script (e.g., Rscript carrot_analysis.R, or open it in RStudio and run top to bottom). Running the script will reproduce: The corrected split-split-plot ANOVA for all 12 proximate and anti-nutrient traits, alongside a naive single-error ANOVA for comparison Estimated marginal means and Tukey-adjusted pairwise comparisons for the one significant effect (phytate: tillage x manure interaction) Descriptive tables (mean +/- standard error by variety, manure rate, and tillage) Phytate:mineral molar ratio calculations All five figures used in the manuscript (proximate boxplots, anti-nutrient boxplots, the phytate interaction plot, PCA biplot, correlation heatmap) All outputs are written to a carrot_analysis_output/ folder created automatically alongside the input files.